CHAPTER 2
AN OVERVIEW OF BIOLOGICAL BASICS – ENGINEER’S PERSPECTIVE
I.
2.1 ARE ALL CELLS THE SAME?
a. 2.2.1 - Microbial Diversity (p. 11-12)
i. Temperature – psychrophiles (<20 C), mesophiles (20-50 C),
thermophiles (>50 C)
ii. Oxygen (aerobic), anaerobic (obligate), facultative
iii. Nutrients – cyanobacteria are photosynthetic and also nitrogen
fixers (convert N2 into NH3)
iv. Shapes – spherical/elliptical (coccus, cocci), cylindrical/rod
(bacillus, bacilli), spiral (spirillum, spirilla).
b. 2.1.2 - Naming Cells (p. 12-14)
i. Genus species srains substrains, e.g., Eschericia coli K12
1. genus - group of related species
2. species – organisms that are substantially alike
3. strains/substrain – variation within species
ii. Two primary cell types – (1) prokaryotic and (2) eucaryotic
1. prokaryotes – (Table 2.1, 2,2)–no nuclear membrane
a. eubacteria and archaebacteria (Table2.2)
2. eucaryotes – (Table 2.1, 2,2)–nuclear membrane, organelles
c. 2.1.3 – Viruses (p. 14)
i. Need host cell to be functionally active, are NOT free- living
ii. Size – 30 to 200 nm (nano- meters)
iii. DNA or RNA covered by a capsid (protein coat)
iv. Lytic cycle – host cells lyse to release phages
v. Lysogenic cycle - phase DNA is incorporated into the host DNA
and the host continues to multiply in this state
vi. Phages - role in bioprocess technology
1. phage attack on E. coli fermentation to make a
recombinant protein product can be destructive
2. phages can be used as agents to move genetic material into
E. coli.
3. Killed phage preparation has been used as a vaccine
4. Production of virus-like particles that are empty shells
(capsid) used a vaccines
5. Gene therapy – replace virus genetic material with a
desired gene; capsid acts as a Trojan Horse to protect the
gene and to deliver it selectively to a cell type. In this case,
the virus is a biotechnology tool.
f. 2.1.4- Procaryotes (p.15)–0.5 to 3 microns (um) in radius, rapid growth (hrs)
1. Eubacteria- gram stain (Gm+ [B. subtilis], Gm– [E. coli])
a. Gm + better suited to excretion of proteins
b. Figure 2.2 (p. 16) Gm – bacterium with outer
membrane
c. Mycoplasma – (Not Gm + or Gm –), clinically
important (primary atypical pneumonia) and
common contamination of media used industrially
for animal cell culture.
d. Acinomycetes (longand branched hyphae) –
e. Antibiotics source
f. Amylolytic and cellulolytic enzymes (some) for
enzymatic hydrolysis of starch and cellulose (e.g.,
Actinomyces, Thermomonospora, and Streptomyces)
g. Table 2.3 (p. 18) – Bacterial architecture
2. Archaebacteria (p.17) – differ at the molecular level.
a. No peptideglycan, different lipid composition of
cytoplasmic membrane.
b. Methanogens, thermoacidophiles, halobacteria
c. Sources of active enzymes with novel properties.
3. Eucaryotes (p. 19) – yeast 5u, animal 10u, plant 20u
a. Figure 2.3 (p. 19) – Animal and Plant cells
b. Sterols in cytoplasmic membrane strengthen the
structure and make membrane less flexible
c. Animal cells do NOT have cell wall, only
cytoplasmic membrane à animal cells are shear
sensitive, fragile, and complicates the design of
large-scale bioreactors for animal cells
d. Reproduction and components – p. 20-22
e. Fungi - (1) yeasts (Fig. 2.6), (2) molds (Fig. 2.7)
i. Yeasts – Saccharomyces cerevisiae
(anaerobic alcohol formation and aerobic
baker’s yeast production)
ii. Molds – antibiotics, citric acid (Aspergillus
niger), make up a large raction of the
fermentation industry - submerged culture
forms pellets (50 u to 1 mm) can cause
nutrient transfer problems (oxygen), but
pellet formation reduced broth viscosity
which can improve bulk oxygen transfer.
iii. 4 classes: (1) phyco, (2) asco, (3) basidio, and
(4) deuteromycetes (Trichophyton – athlete’s
foot)
f. Algae (p. 24) – diatoms (filter aids), Chlorella
(wastewater treatment with single-cell protein
production), gelling agents such as agar and alginic
acid.
II.
2.2 – CELL CONSTRUCTION (p. 25)
a. 2.2.1 - Introduction – living cell structural elements include: proteins,
nucleic acids, polysaccharides, lipids, and the storage materials including
fats, polyhydroxybutyrate, and glycogen.
b. Biological system – levels of understanding:
i. Molecular (molecular biology, biochemistry)
ii. Cellular (cell biology, microbiology)
iii. Population (microbiology, ecology)
iv. Production (bioprocess engineering)
c. 2.2.2 – Amino Acids and Proteins (p. 26)
i. α−Amino Acids – monomers of proteins, form peptide bonds
1. Table 2.4 (p. 29) Amino acid structure
2. Isoelectric point – protein purification processes
ii. Proteins –
1. 5 categories
a. structural: glycoproteins, collagen, keratin
b. catalytic: enzymes (> 2,000 known)
c. transport: hemoglobin, serum albumin
d. regulatory: hormones (insulin, growth hormones)
e. protective: antibodies, thrombin
2. 3-D structures described at 4- levels of structure (p. 29)
a. primary–linear sequence of amino acids (1-d length)
b. secondary-hydrogen bonding: (1) helixes, (2) sheets
c. tertiary-R- group interactions (covalent, disulfide, H)
d. quaternary-polypeptide chains interacting
3. Antibodies or immunoglobulins (p. 31)
a. immune (Ab-Ag reactions), diagnostic kits, protein
separation schemes, delivery of anticancer drugs
b. one of most important products of biotechnology
c. abzymes – impart catalytic activity to antibodies.
Couple protein engineering to antibodies promises
development of specific catalytic agents.
4. Carbohydrates – 2.2.3 (p. 34)
a. Modulate some chemical signaling-animals/plants
b. Monosaccharides: 3-9 C-atoms. Tale 2.5 (p. 35)
i. D-ribose, deoxyribose in RNA, DNA
ii. glucose, sucrose (plant sugar), lactose (milk
and whey)
c. polyscaaharides: > 2 monosaccharides (p. 37)
i. biochemical engg-> polysaccharide industry
(dextrins – branched sections o famylopectin
are used as thickeners)
ii. cellulose = chain of D-glucose monomers
linked by β-1,4 glycosidic bonds. Resistant
to enzymatic hydrolysis. Interest in
converting cellulose wastes into fuels or
chemicals.
5. Lipids, Fats, and Steroids – 2.2.2 (p. 38)
a. Lipids – present in nonaqueous biological phases
(plasma membranes); fatty acid composition
i. Fats – lipids that serve as biological fuel
storage
ii. Phospholipids – key membrane component
iii. Polyhydroxyankanoates (PHA), e.g.,
polyhydroxybutyrate (PHB), a storage
product in some cells. (p. 40)
iv. Steroids - hormones (10-8 M), cholesterol,
cortisone, estrognen, progesterone
1. Commercial production depends on
microbial conversion, because the
large number of asymmetric centers
makes total synthesis difficult (p.40)
6. Nucleic Acids, RNA, DNA – 2.2.5 (p. 40)
a. Nucleic Acids – reproduction of living cells
b. DNA – stores & preserves genetic information
c. RNA – central role in protein synthesis
i. m-RNA (p. 46), short half- life
ii. t-RNA, stable
iii. r-RNA, major component of ribosomes
d. Nucleotides –
i. Building blocks of DNA and RNA
ii. Store Energy – ATP, ADP
iii. Reducing power - NAD, NADP
e. Plasmids – circular DNA in cytoplasm,
nonchromosomal, automonous, self-replicating.
f. Easily moved in and out of cells, and used for
genetic engineering
III.
2.3 - CELL NUTRIENTS (p. 46)
a. Introduction – 2.3.1 (p. 46)
i. Cell composition different from its environment (due to
semipermeable membrane and energy expenditure to keep it away
from thermodynamic equilibrium.
ii. Table 2.7 (p. 48) – 80% water
iii. Macronutrients – required at >10-4 M (C,N,O,H,S,P, Mg, K)
iv. Micronutrients – required at < 10-4 M (Mo, Zn, Cu, Mn, Ca, Na,
vitamins, growth hormones, metabolic precursors)
b. Macronutrients – 2.3.2 (p. 49), see Tables 2.8 (p. 49) and 2.9 (p.50)
i. Carbon Source – (1) Heterotrophs use organic compounds ; (2)
Autotrophs use CO2 . See Table 2.8 (p. 49)
1. Most common for industrial fermentations – molasses
(sucrose), starch (glucose, dextrin), corn syrup, and waste
sulfite liquor (glucose). (methanol, ethanol, and methane
are also cheap carbon sources for some fermentations)
ii. Energy Sources – (1) Chemo (reduced inorganic chemicals), (2)
photo (light energy)
c. Micronutrients – 2.3.3 (p. 50)
i. Iron – plays a regulatory role in some fermentation processes
1. deficiency required for excretionof riboflavin by Ashbya
gosypii
2. conc. Regulates penicillin production by P. chrysogenum
3. Mn – enzyme co- factor, plays role in regulation of
secondary metabolism and excretion of primary metabolites
ii. Copper –in certain respiratory-chain components & enzymes
1. deficiency stimulates penicillin and citric acid production
iii. Cobalt–vitamin B12 . Required in propionic bacteria& methanogens
iv. Mo- nitrate reductase and nitrogenase & for growth on NO3 and N2
as sole source of nitrogen
v. Ca – co-factor for amylases and some proteases
vi. Vitamins – required at concs. of 10-6 to 10-12 M
d. Growth Media – 2.3.4 (p. 52) See Table 2.10 (p. 52)
i. Defined media - specific amounts of pure chemical compounds
with known chemical compositions.
ii. Complex media – contain natural compounds whose chemical
composition is not exactly known (e.g., yeast extract, peptone,
molasses, or corn steep liquor). Usually provides growth factors,
vitamins, hormones, and trace elements often resulting in higher
cell yields.